• Proceedings of the Korean Vacuum Society Conference
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• 2011.08a
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• pp.107-107
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• 2011

Supramolecular structures of anthraquinone molecules on a metallic surface are studied using scanning tunneling microscope (STM) under ultrahigh-vacuum conditions. When we deposited anthraquinone molecules on Au(111) substrate, the molecules formed three different phases (Chevron type, tetragon type and disordered type) on the surface. Based on our STM measurements, we proposed models for the observed molecular structures. Chevrons are consisted of several molecular chains, which make well-ordered two-dimensional islands by some weak interrow interactions and we could observe tetragon structures which make array of (111) metallic surface. each molecular rows in the chevrons are stabilized by two parallel O-H hydrogen bonds and disordered structures are observed 1-dimensional phase with hydrogen bond. First-principles calculations based on density functional theory are performed to reproduce the proposed models. Distances and energy gains for each intermolecular bond are estimated. In this presentation, we explain possible origins of these molecular structures in terms of hydrogen bonds, Van der Waals interactions and molecule-substrate interactions.

• Journal of the Korean Chemical Society
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• v.7 no.4
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• pp.293-298
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• 1963

The crystal structure of ethylenediamine dihydrochloride has been determined by the two-dimensional Patterson methods and refined by two-dimensional Fourier syntheses. The unit cell dimensions are a = 4.44${\pm}$0.02, b = 6.88${\pm}$0.02, c = 9.97${\pm}$0.02 ${\AA}$, ${\beta}$ = 92${\pm}$$1^{\circ}$. The space group is $P2_1_{/c}$. The carbon and nitrogen atoms in the ethylenediamine itself lie on one plane and its structure has a trans-form with a centre of symmetry in it, and C-C distance of 1.54 ${\AA}$, C-N distance of 1.48${\AA}$ and C-C-N bond angle of $109.07^{\circ}$. The molecules are linked by N-H${\cdots}$Cl hydrogen bonds with distance of 3.14, 3.16 and 3.22 ${\AA}$ forming three dimensional network. The values of reliability factor for F(okl), F(hol) and F(hko) are 0.11, 0.10 and 0.09 respectively.

• Proceedings of the Polymer Society of Korea Conference
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• 2006.10a
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• pp.297-297
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• 2006

Recently columnar liquid crystals have been studied due to their possible application to organic conducting materials. Supramolecular columnar liquid crystals consist of mesogenic unit which can aggregate into discs that will make up the columns which associate to form a two-dimensional network. In this study, we prepared supramolecular columnar liquid crystals containing hydrogen bonding between carboxylic acid and, pyridine moieties. Thermal and structural properties of prepared complexe were investigated, and it exhibited hexagonal columnar structure ($Col_{h}$) at room temperature.

• Journal of the Korean Magnetic Resonance Society
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• v.5 no.2
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• pp.130-137
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• 2001

Backbone dynamics of the catalytic residues in free and steroid-bound $\Delta$$^{5}$ -3- ketosteroid isomerase from Pseudomonas testosteroni has been examined by $^{15}$ N relaxation measurements. The relaxation data were analyzed using the model-free formalism to extract the model-free parameters (S$^2$, $\tau$$_{e}$, and R$_{ex}$). Tyr-34 and Asp-99 exhibit enhanced high-frequency (pico- to nanosecond) internal motions in the free enzyme, which are restricted upon ligand binding, while Asp-38 experiences severe restriction of the internal motions in the fee enzyme, suggesting that Tyr-14 and Asp-99 are more actively involved in the ligand binding than Asp-38. The results also indicate that the H-bond network in the catalytic cavity might be slightly strengthened upon ligand binding, which may have some implications on the enzyme mechanism.he enzyme mechanism.m.

• Bulletin of the Korean Chemical Society
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• v.3 no.1
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• pp.9-13
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• 1982

Sulfametrole, $C_9H_{10}N_4O_3S_2$, crystallizes in the monoclinic system, space group $P2_1/n$ , with a = 8.145(2), b = 16.505(4), c = 9.637(1)${\AA},{\beta}=103.72(1)^{\circ},D_m=1.52gcm^{-3}$,Z=4.Intensities for 3594(2143 observed) unique reflections were measured on a four-circle diffractometer with Mo $K{\alpha}$ radiation $({\lambda}=0.71069{\AA})$. The structure was solved by direct method and refined by full-matrix least squares to a final R of 0.070. The geometrical features of the thiadiazole ring indicate some ${pi}$-electron delocalization inside the ring. The least squares planes defined by the benzene and thiadiazole rings are nearly perpendicular to each other(dihedral angle; $93.9^{\circ}$ ). All the potential hydrogen-bond donor atoms in the molecule, N(1) and N(2), are included in the hydrogen bonding. The molecules through hydrogen bonding form three dimensional network.

• Bulletin of the Korean Chemical Society
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• v.5 no.4
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• pp.158-162
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• 1984

The crystal structure of chloramphenicol base, $C_9H_{l2}N_2O_4$, the deacylated base of antibiotic chloramphenicol, has been determined by X-ray diffraction techniques using diffractometer data obtained by the ${\omega}-2{\theta}$ scan technique with CuK${\alpha}$ radiation from a crystal with space group symmetry $P2_12_12_1$ and unit cell parameters a = 22.322(6), b = 7.535(6), c = 5.781(5) ${\AA}$. The structure was solved by direct methods and refined by full-matrix least-squares to a final R = 0.051 for the 573 observed reflections. The overall conformation of the base is quite different from those of the chloramphenicol congeners which are similar despite the presence of many rotatable single bonds. The propane chain in the base is bent with respect to the phenyl ring, while it is extended in the chloramphenicol congeners. There is no intramolecular hydrogen bond between the hydroxyl groups of the propanediol moiety. All of the molecules in the crystal lattice are connected by a three-dimensional hydrogen bonding network.

• Journal of Ginseng Research
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• v.44 no.5
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• pp.690-696
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• 2020

Background: As the main metabolites of ginsenosides, 20(S, R)-protopanaxadiol [PPD(S, R)] and 20(S, R)-protopanaxatriol [PPT(S, R)] are the structural basis response to a series of pharmacological effects of their parent components. Although the estrogenicity of several ginsenosides has been confirmed, however, the underlying mechanisms of their estrogenic effects are still largely unclear. In this work, PPD(S, R) and PPT(S, R) were assessed for their ability to bind and activate human estrogen receptor α (hERα) by a combination of in vitro and in silico analysis. Methods: The recombinant hERα ligand-binding domain (hERα-LBD) was expressed in E. coli strain. The direct binding interactions of ginsenosides with hERα-LBD and their ERα agonistic potency were investigated by fluorescence polarization and reporter gene assays, respectively. Then, molecular dynamics simulations were carried out to simulate the binding modes between ginsenosides and hERα-LBD to reveal the structural basis for their agonist activities toward receptor. Results: Fluorescence polarization assay revealed that PPD(S, R) and PPT(S, R) could bind to hERα-LBD with moderate affinities. In the dual luciferase reporter assay using transiently transfected MCF-7 cells, PPD(S, R) and PPT(S, R) acted as agonists of hERα. Molecular docking results showed that these ginsenosides adopted an agonist conformation in the flexible hydrophobic ligand-binding pocket. The stereostructure of C-20 hydroxyl group and the presence of C-6 hydroxyl group exerted significant influence on the hydrogen bond network and steric hindrance, respectively. Conclusion: This work may provide insight into the chemical and pharmacological screening of novel therapeutic agents from ginsenosides.

• Journal of the Korean Chemical Society
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• v.9 no.3
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• pp.128-133
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• 1965

Hydrazonium diphosphate crystallizes with the space-group symmetry $P2_1/C.$ There are two formular units of $N_2H_6H_4(PO_4)_2$ in the unit cell, for which $a = 4.52{\pm}0.02, b = 8.06{\pm}0.03, c = 10.74{\pm}0.03{\AA}\;and\; {\beta} = 100{\pm}0.5^{\circ}.$ The determination of the crystal structure was carried out by means of Patterson, Fourier and difference syntheses. The phosphate group has configuration of nearly regular tetrahedron with the mean P-O distance of $1.55{\AA}.$ The N-N distance found is $1.40{\AA},$ which corresponds to previously reported values for the $N_2H_6^{++} \;ion \;in\; N_2H_6SO_4.$ A molecule has a transform with a center of symmetry in it. Each nitrogen atom forms three hydrogen bonds with the N…O distances 2.62, 2.79 and $2.89{\AA}.$ And a O…O hydrogen bond between different phosphate groups is found with the distance $2.63{\AA}.$ The structure is held together by three-dimensional network of the strong hydrogen bonds.

• Journal of the Korean Chemical Society
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• v.47 no.2
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• pp.104-108
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• 2003

The reaction of $[Cu(L)]Cl_2{\cdot}H_2O(L=3,14-dimethyl-2,6,13,17-tetraazatricyclo[14,4,0^{1.18},0^{7.12}]docosane)$ with 2,5-pyridinedicarboxylate(pdc) led to the formation of $[Cu(L)(H_2O)](pdc){\cdot}6H_2O(1)$. The structure was characterized by X-ray crystallography and spectroscopic method. The coordination geometry around the copper atom is a distorted square-pyramid with four secondary amines of the macrocycle occupying the basal sites and a water molecule at the axial position. Intermolecular hydrogen bonds in 1 form a three-dimensional molecular network.

• Journal of the Korean Ceramic Society
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• v.41 no.9
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• pp.696-702
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• 2004

Lifetime of excited electronic states inside the 4f configuration of rare-earth elements embedded in chalcogenide glasses is very sensitive to medium-range structural changes of the host glasses. We have measured lifetimes of the 1.6$\mu\textrm{m}$ emission originating from Pr$\^$3+/ : ($^3$F$_3$, $^3$F$_4$)\longrightarrow$^3$H$_4$ transition in amorphous chalcogenide samples consisting of Ge, Sb, and Se elements. The measured lifetimes fumed out to have their maximum at the mean coordination number of -2.67, which arises accordingly from structural changes of the host glasses from 2 dimensional layers to 3 dimensional networks. This new finding supports that the so-called topological structure model together with chemically ordered network model is adequate to explain relationship between the emission properties of rare-earth elements and the medium-range structures of amorphous chalcogenide hosts with a large covalent bond nature. Thus, it is validated to predict site distribution and lifetime of rare-earth elements doped in chalcogenide glasses simply based on their mean coordination number.